gt-4v1eo: Implement ephemeral protos - cook formulas inline

Major refactor of molecular chemistry to make protos ephemeral:
- Formulas are now cooked directly to in-memory TemplateSubgraph
- No more proto beads stored in the database

Changes:
- cook.go: Add cookFormulaToSubgraph() and resolveAndCookFormula()
  for in-memory formula cooking
- template.go: Add VarDefs field to TemplateSubgraph for default
  value handling, add extractRequiredVariables() and
  applyVariableDefaults() helpers
- pour.go: Try formula loading first for any name (not just mol-)
- wisp.go: Same pattern as pour
- mol_bond.go: Use resolveOrCookToSubgraph() for in-memory subgraphs
- mol_catalog.go: List formulas from disk instead of DB proto beads
- mol_distill.go: Output .formula.json files instead of proto beads

Flow: Formula (.formula.json) -> pour/wisp (cook inline) -> Mol/Wisp

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/cook.go

@@ -262,6 +262,257 @@ type cookFormulaResult struct {
 	Created int
 }
 
+// cookFormulaToSubgraph creates an in-memory TemplateSubgraph from a resolved formula.
+// This is the ephemeral proto implementation - no database storage.
+// The returned subgraph can be passed directly to cloneSubgraph for instantiation.
+func cookFormulaToSubgraph(f *formula.Formula, protoID string) (*TemplateSubgraph, error) {
+	// Map step ID -> created issue
+	issueMap := make(map[string]*types.Issue)
+
+	// Collect all issues and dependencies
+	var issues []*types.Issue
+	var deps []*types.Dependency
+
+	// Create root proto epic
+	rootIssue := &types.Issue{
+		ID:          protoID,
+		Title:       f.Formula, // Title is the original formula name
+		Description: f.Description,
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeEpic,
+		IsTemplate:  true,
+		CreatedAt:   time.Now(),
+		UpdatedAt:   time.Now(),
+	}
+	issues = append(issues, rootIssue)
+	issueMap[protoID] = rootIssue
+
+	// Collect issues for each step (use protoID as parent for step IDs)
+	collectStepsToSubgraph(f.Steps, protoID, issueMap, &issues, &deps)
+
+	// Collect dependencies from depends_on
+	stepIDMapping := make(map[string]string)
+	for _, step := range f.Steps {
+		collectStepIDMappings(step, protoID, stepIDMapping)
+	}
+	for _, step := range f.Steps {
+		collectDependenciesToSubgraph(step, stepIDMapping, &deps)
+	}
+
+	return &TemplateSubgraph{
+		Root:         rootIssue,
+		Issues:       issues,
+		Dependencies: deps,
+		IssueMap:     issueMap,
+	}, nil
+}
+
+// collectStepsToSubgraph collects issues and dependencies for steps and their children.
+// This is the in-memory version that doesn't create labels (since those require DB).
+func collectStepsToSubgraph(steps []*formula.Step, parentID string, issueMap map[string]*types.Issue,
+	issues *[]*types.Issue, deps *[]*types.Dependency) {
+
+	for _, step := range steps {
+		// Generate issue ID (formula-name.step-id)
+		issueID := fmt.Sprintf("%s.%s", parentID, step.ID)
+
+		// Determine issue type
+		issueType := types.TypeTask
+		if step.Type != "" {
+			switch step.Type {
+			case "task":
+				issueType = types.TypeTask
+			case "bug":
+				issueType = types.TypeBug
+			case "feature":
+				issueType = types.TypeFeature
+			case "epic":
+				issueType = types.TypeEpic
+			case "chore":
+				issueType = types.TypeChore
+			}
+		}
+
+		// If step has children, it's an epic
+		if len(step.Children) > 0 {
+			issueType = types.TypeEpic
+		}
+
+		// Determine priority
+		priority := 2
+		if step.Priority != nil {
+			priority = *step.Priority
+		}
+
+		issue := &types.Issue{
+			ID:             issueID,
+			Title:          step.Title, // Keep {{variables}} for substitution at pour time
+			Description:    step.Description,
+			Status:         types.StatusOpen,
+			Priority:       priority,
+			IssueType:      issueType,
+			Assignee:       step.Assignee,
+			IsTemplate:     true,
+			CreatedAt:      time.Now(),
+			UpdatedAt:      time.Now(),
+			SourceFormula:  step.SourceFormula,  // Source tracing (gt-8tmz.18)
+			SourceLocation: step.SourceLocation, // Source tracing (gt-8tmz.18)
+		}
+
+		// Store labels in the issue's Labels field for in-memory use
+		issue.Labels = append(issue.Labels, step.Labels...)
+
+		// Add gate label for waits_for field (bd-j4cr)
+		if step.WaitsFor != "" {
+			gateLabel := fmt.Sprintf("gate:%s", step.WaitsFor)
+			issue.Labels = append(issue.Labels, gateLabel)
+		}
+
+		*issues = append(*issues, issue)
+		issueMap[issueID] = issue
+
+		// Add parent-child dependency
+		*deps = append(*deps, &types.Dependency{
+			IssueID:     issueID,
+			DependsOnID: parentID,
+			Type:        types.DepParentChild,
+		})
+
+		// Recursively collect children
+		if len(step.Children) > 0 {
+			collectStepsToSubgraph(step.Children, issueID, issueMap, issues, deps)
+		}
+	}
+}
+
+// collectStepIDMappings builds a map from step ID to full issue ID
+func collectStepIDMappings(step *formula.Step, parentID string, mapping map[string]string) {
+	issueID := fmt.Sprintf("%s.%s", parentID, step.ID)
+	mapping[step.ID] = issueID
+
+	for _, child := range step.Children {
+		collectStepIDMappings(child, issueID, mapping)
+	}
+}
+
+// collectDependenciesToSubgraph collects blocking dependencies from depends_on and needs fields.
+func collectDependenciesToSubgraph(step *formula.Step, idMapping map[string]string, deps *[]*types.Dependency) {
+	issueID := idMapping[step.ID]
+
+	// Process depends_on field
+	for _, depID := range step.DependsOn {
+		depIssueID, ok := idMapping[depID]
+		if !ok {
+			continue // Will be caught during validation
+		}
+
+		*deps = append(*deps, &types.Dependency{
+			IssueID:     issueID,
+			DependsOnID: depIssueID,
+			Type:        types.DepBlocks,
+		})
+	}
+
+	// Process needs field (bd-hr39) - simpler alias for sibling dependencies
+	for _, needID := range step.Needs {
+		needIssueID, ok := idMapping[needID]
+		if !ok {
+			continue // Will be caught during validation
+		}
+
+		*deps = append(*deps, &types.Dependency{
+			IssueID:     issueID,
+			DependsOnID: needIssueID,
+			Type:        types.DepBlocks,
+		})
+	}
+
+	// Recursively handle children
+	for _, child := range step.Children {
+		collectDependenciesToSubgraph(child, idMapping, deps)
+	}
+}
+
+// resolveAndCookFormula loads a formula by name, resolves it, applies all transformations,
+// and returns an in-memory TemplateSubgraph ready for instantiation.
+// This is the main entry point for ephemeral proto cooking.
+func resolveAndCookFormula(formulaName string, searchPaths []string) (*TemplateSubgraph, error) {
+	// Create parser with search paths
+	parser := formula.NewParser(searchPaths...)
+
+	// Load formula by name
+	f, err := parser.LoadByName(formulaName)
+	if err != nil {
+		return nil, fmt.Errorf("loading formula %q: %w", formulaName, err)
+	}
+
+	// Resolve inheritance
+	resolved, err := parser.Resolve(f)
+	if err != nil {
+		return nil, fmt.Errorf("resolving formula %q: %w", formulaName, err)
+	}
+
+	// Apply control flow operators (gt-8tmz.4) - loops, branches, gates
+	controlFlowSteps, err := formula.ApplyControlFlow(resolved.Steps, resolved.Compose)
+	if err != nil {
+		return nil, fmt.Errorf("applying control flow to %q: %w", formulaName, err)
+	}
+	resolved.Steps = controlFlowSteps
+
+	// Apply advice transformations (gt-8tmz.2)
+	if len(resolved.Advice) > 0 {
+		resolved.Steps = formula.ApplyAdvice(resolved.Steps, resolved.Advice)
+	}
+
+	// Apply expansion operators (gt-8tmz.3)
+	if resolved.Compose != nil && (len(resolved.Compose.Expand) > 0 || len(resolved.Compose.Map) > 0) {
+		expandedSteps, err := formula.ApplyExpansions(resolved.Steps, resolved.Compose, parser)
+		if err != nil {
+			return nil, fmt.Errorf("applying expansions to %q: %w", formulaName, err)
+		}
+		resolved.Steps = expandedSteps
+	}
+
+	// Apply aspects from compose.aspects (gt-8tmz.5)
+	if resolved.Compose != nil && len(resolved.Compose.Aspects) > 0 {
+		for _, aspectName := range resolved.Compose.Aspects {
+			aspectFormula, err := parser.LoadByName(aspectName)
+			if err != nil {
+				return nil, fmt.Errorf("loading aspect %q: %w", aspectName, err)
+			}
+			if aspectFormula.Type != formula.TypeAspect {
+				return nil, fmt.Errorf("%q is not an aspect formula (type=%s)", aspectName, aspectFormula.Type)
+			}
+			if len(aspectFormula.Advice) > 0 {
+				resolved.Steps = formula.ApplyAdvice(resolved.Steps, aspectFormula.Advice)
+			}
+		}
+	}
+
+	// Cook to in-memory subgraph, including variable definitions for default handling
+	return cookFormulaToSubgraphWithVars(resolved, resolved.Formula, resolved.Vars)
+}
+
+// cookFormulaToSubgraphWithVars creates an in-memory subgraph with variable info attached
+func cookFormulaToSubgraphWithVars(f *formula.Formula, protoID string, vars map[string]*formula.VarDef) (*TemplateSubgraph, error) {
+	subgraph, err := cookFormulaToSubgraph(f, protoID)
+	if err != nil {
+		return nil, err
+	}
+	// Attach variable definitions to the subgraph for default handling during pour
+	// Convert from *VarDef to VarDef for simpler handling
+	if vars != nil {
+		subgraph.VarDefs = make(map[string]formula.VarDef)
+		for k, v := range vars {
+			if v != nil {
+				subgraph.VarDefs[k] = *v
+			}
+		}
+	}
+	return subgraph, nil
+}
+
 // cookFormula creates a proto bead from a resolved formula.
 // protoID is the final ID for the proto (may include a prefix).
 func cookFormula(ctx context.Context, s storage.Storage, f *formula.Formula, protoID string) (*cookFormulaResult, error) {

cmd/bd/mol_bond.go

@@ -5,7 +5,6 @@ import (
 	"fmt"
 	"os"
 	"strings"
-	"time"
 
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/formula"
@@ -208,38 +207,27 @@ func runMolBond(cmd *cobra.Command, args []string) {
 	}
 
 	// Resolve both operands - can be issue IDs or formula names
-	// Formula names are cooked inline to ephemeral protos (gt-8tmz.25)
-	issueA, cookedA, err := resolveOrCookFormula(ctx, store, args[0], actor)
+	// Formula names are cooked inline to in-memory subgraphs (gt-4v1eo)
+	subgraphA, cookedA, err := resolveOrCookToSubgraph(ctx, store, args[0])
 	if err != nil {
 		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
 		os.Exit(1)
 	}
-	issueB, cookedB, err := resolveOrCookFormula(ctx, store, args[1], actor)
+	subgraphB, cookedB, err := resolveOrCookToSubgraph(ctx, store, args[1])
 	if err != nil {
-		// Clean up first cooked formula if second one fails
-		if cookedA {
-			_ = deleteProtoSubgraph(ctx, store, issueA.ID)
-		}
 		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
 		os.Exit(1)
 	}
 
-	// Track cooked formulas for cleanup (ephemeral protos deleted after use)
-	cleanupCooked := func() {
-		if cookedA {
-			_ = deleteProtoSubgraph(ctx, store, issueA.ID)
-		}
-		if cookedB {
-			_ = deleteProtoSubgraph(ctx, store, issueB.ID)
-		}
-	}
-
+	// No cleanup needed - in-memory subgraphs don't pollute the DB
+	issueA := subgraphA.Root
+	issueB := subgraphB.Root
 	idA := issueA.ID
 	idB := issueB.ID
 
 	// Determine operand types
-	aIsProto := isProto(issueA)
-	bIsProto := isProto(issueB)
+	aIsProto := issueA.IsTemplate || cookedA
+	bIsProto := issueB.IsTemplate || cookedB
 
 	// Dispatch based on operand types
 	// All operations use the main store; wisp flag determines ephemeral vs persistent
@@ -247,17 +235,27 @@ func runMolBond(cmd *cobra.Command, args []string) {
 	switch {
 	case aIsProto && bIsProto:
 		// Compound protos are templates - always persistent
+		// Note: Proto+proto bonding from formulas is a DB operation, not in-memory
 		result, err = bondProtoProto(ctx, store, issueA, issueB, bondType, customTitle, actor)
 	case aIsProto && !bIsProto:
-		result, err = bondProtoMol(ctx, store, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+		// Pass subgraph directly if cooked from formula
+		if cookedA {
+			result, err = bondProtoMolWithSubgraph(ctx, store, subgraphA, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+		} else {
+			result, err = bondProtoMol(ctx, store, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+		}
 	case !aIsProto && bIsProto:
-		result, err = bondMolProto(ctx, store, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+		// Pass subgraph directly if cooked from formula
+		if cookedB {
+			result, err = bondProtoMolWithSubgraph(ctx, store, subgraphB, issueB, issueA, bondType, vars, childRef, actor, wisp, pour)
+		} else {
+			result, err = bondMolProto(ctx, store, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+		}
 	default:
 		result, err = bondMolMol(ctx, store, issueA, issueB, bondType, actor)
 	}
 
 	if err != nil {
-		cleanupCooked()
 		fmt.Fprintf(os.Stderr, "Error bonding: %v\n", err)
 		os.Exit(1)
 	}
@@ -265,10 +263,6 @@ func runMolBond(cmd *cobra.Command, args []string) {
 	// Schedule auto-flush - wisps are in main DB now, but JSONL export skips them
 	markDirtyAndScheduleFlush()
 
-	// Clean up ephemeral protos after successful bond
-	// These were only needed to get the proto structure; the spawned issues persist
-	cleanupCooked()
-
 	if jsonOutput {
 		outputJSON(result)
 		return
@@ -284,9 +278,6 @@ func runMolBond(cmd *cobra.Command, args []string) {
 	} else if pour {
 		fmt.Printf("  Phase: liquid (persistent, Wisp=false)\n")
 	}
-	if cookedA || cookedB {
-		fmt.Printf("  Ephemeral protos cleaned up after use.\n")
-	}
 }
 
 // isProto checks if an issue is a proto (has the template label)
@@ -394,11 +385,21 @@ func bondProtoProto(ctx context.Context, s storage.Storage, protoA, protoB *type
 
 // bondProtoMol bonds a proto to an existing molecule by spawning the proto.
 // If childRef is provided, generates custom IDs like "parent.childref" (dynamic bonding).
+// protoSubgraph can be nil if proto is from DB (will be loaded), or pre-loaded for formulas.
 func bondProtoMol(ctx context.Context, s storage.Storage, proto, mol *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, wispFlag, pourFlag bool) (*BondResult, error) {
-	// Load proto subgraph
-	subgraph, err := loadTemplateSubgraph(ctx, s, proto.ID)
-	if err != nil {
-		return nil, fmt.Errorf("loading proto: %w", err)
+	return bondProtoMolWithSubgraph(ctx, s, nil, proto, mol, bondType, vars, childRef, actorName, wispFlag, pourFlag)
+}
+
+// bondProtoMolWithSubgraph is the internal implementation that accepts a pre-loaded subgraph.
+func bondProtoMolWithSubgraph(ctx context.Context, s storage.Storage, protoSubgraph *TemplateSubgraph, proto, mol *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, wispFlag, pourFlag bool) (*BondResult, error) {
+	// Use provided subgraph or load from DB
+	subgraph := protoSubgraph
+	if subgraph == nil {
+		var err error
+		subgraph, err = loadTemplateSubgraph(ctx, s, proto.ID)
+		if err != nil {
+			return nil, fmt.Errorf("loading proto: %w", err)
+		}
 	}
 
 	// Check for missing variables
@@ -564,18 +565,31 @@ func resolveOrDescribe(ctx context.Context, s storage.Storage, operand string) (
 	return nil, f.Formula, nil
 }
 
-// resolveOrCookFormula tries to resolve an operand as an issue ID.
-// If not found and it looks like a formula name, cooks the formula inline.
-// Returns the issue, whether it was cooked (ephemeral proto), and any error.
+// resolveOrCookToSubgraph tries to resolve an operand as an issue ID or formula.
+// If it's an issue, loads the subgraph from DB. If it's a formula, cooks inline to subgraph.
+// Returns the subgraph, whether it was cooked from formula, and any error.
 //
-// This implements gt-8tmz.25: formula names are cooked inline as ephemeral protos.
-func resolveOrCookFormula(ctx context.Context, s storage.Storage, operand string, actorName string) (*types.Issue, bool, error) {
+// This implements gt-4v1eo: formulas are cooked to in-memory subgraphs (no DB storage).
+func resolveOrCookToSubgraph(ctx context.Context, s storage.Storage, operand string) (*TemplateSubgraph, bool, error) {
 	// First, try to resolve as an existing issue
 	id, err := utils.ResolvePartialID(ctx, s, operand)
 	if err == nil {
 		issue, err := s.GetIssue(ctx, id)
 		if err == nil {
-			return issue, false, nil
+			// Check if it's a proto (template)
+			if isProto(issue) {
+				subgraph, err := loadTemplateSubgraph(ctx, s, id)
+				if err != nil {
+					return nil, false, fmt.Errorf("loading proto subgraph '%s': %w", id, err)
+				}
+				return subgraph, false, nil
+			}
+			// It's a molecule, not a proto - wrap it as a single-issue subgraph
+			return &TemplateSubgraph{
+				Root:     issue,
+				Issues:   []*types.Issue{issue},
+				IssueMap: map[string]*types.Issue{issue.ID: issue},
+			}, false, nil
 		}
 	}
 
@@ -584,72 +598,13 @@ func resolveOrCookFormula(ctx context.Context, s storage.Storage, operand string
 		return nil, false, fmt.Errorf("'%s' not found (not an issue ID or formula name)", operand)
 	}
 
-	// Try to load and cook the formula
-	parser := formula.NewParser()
-	f, err := parser.LoadByName(operand)
+	// Try to cook formula inline to in-memory subgraph (gt-4v1eo)
+	subgraph, err := resolveAndCookFormula(operand, nil)
 	if err != nil {
 		return nil, false, fmt.Errorf("'%s' not found as issue or formula: %w", operand, err)
 	}
 
-	// Resolve formula (inheritance, etc)
-	resolved, err := parser.Resolve(f)
-	if err != nil {
-		return nil, false, fmt.Errorf("resolving formula '%s': %w", operand, err)
-	}
-
-	// Apply control flow operators (gt-8tmz.4)
-	controlFlowSteps, err := formula.ApplyControlFlow(resolved.Steps, resolved.Compose)
-	if err != nil {
-		return nil, false, fmt.Errorf("applying control flow to '%s': %w", operand, err)
-	}
-	resolved.Steps = controlFlowSteps
-
-	// Apply advice transformations (gt-8tmz.2)
-	if len(resolved.Advice) > 0 {
-		resolved.Steps = formula.ApplyAdvice(resolved.Steps, resolved.Advice)
-	}
-
-	// Apply expansion operators (gt-8tmz.3)
-	if resolved.Compose != nil && (len(resolved.Compose.Expand) > 0 || len(resolved.Compose.Map) > 0) {
-		expandedSteps, err := formula.ApplyExpansions(resolved.Steps, resolved.Compose, parser)
-		if err != nil {
-			return nil, false, fmt.Errorf("applying expansions to '%s': %w", operand, err)
-		}
-		resolved.Steps = expandedSteps
-	}
-
-	// Apply aspects (gt-8tmz.5)
-	if resolved.Compose != nil && len(resolved.Compose.Aspects) > 0 {
-		for _, aspectName := range resolved.Compose.Aspects {
-			aspectFormula, err := parser.LoadByName(aspectName)
-			if err != nil {
-				return nil, false, fmt.Errorf("loading aspect '%s': %w", aspectName, err)
-			}
-			if aspectFormula.Type != formula.TypeAspect {
-				return nil, false, fmt.Errorf("'%s' is not an aspect formula (type=%s)", aspectName, aspectFormula.Type)
-			}
-			if len(aspectFormula.Advice) > 0 {
-				resolved.Steps = formula.ApplyAdvice(resolved.Steps, aspectFormula.Advice)
-			}
-		}
-	}
-
-	// Cook the formula to create an ephemeral proto
-	// Use a unique ID to avoid collision with existing protos
-	// Format: _ephemeral-<formula>-<timestamp> (underscore prefix marks it as ephemeral)
-	protoID := fmt.Sprintf("_ephemeral-%s-%d", resolved.Formula, time.Now().UnixNano())
-	result, err := cookFormula(ctx, s, resolved, protoID)
-	if err != nil {
-		return nil, false, fmt.Errorf("cooking formula '%s': %w", operand, err)
-	}
-
-	// Load the cooked proto
-	issue, err := s.GetIssue(ctx, result.ProtoID)
-	if err != nil {
-		return nil, false, fmt.Errorf("loading cooked proto '%s': %w", result.ProtoID, err)
-	}
-
-	return issue, true, nil
+	return subgraph, true, nil
 }
 
 // looksLikeFormulaName checks if an operand looks like a formula name.

cmd/bd/mol_catalog.go

@@ -1,84 +1,134 @@
 package main
 
 import (
-	"encoding/json"
 	"fmt"
-	"os"
+	"sort"
 	"strings"
 
 	"github.com/spf13/cobra"
-	"github.com/steveyegge/beads/internal/rpc"
-	"github.com/steveyegge/beads/internal/types"
 	"github.com/steveyegge/beads/internal/ui"
 )
 
+// CatalogEntry represents a formula in the catalog.
+type CatalogEntry struct {
+	Name        string   `json:"name"`
+	Type        string   `json:"type"`
+	Description string   `json:"description"`
+	Source      string   `json:"source"`
+	Steps       int      `json:"steps"`
+	Vars        []string `json:"vars,omitempty"`
+}
+
 var molCatalogCmd = &cobra.Command{
 	Use:     "catalog",
 	Aliases: []string{"list", "ls"},
-	Short:   "List available molecules",
-	Run: func(cmd *cobra.Command, args []string) {
-		ctx := rootCtx
-		var molecules []*types.Issue
+	Short:   "List available molecule formulas",
+	Long: `List formulas available for bd pour / bd wisp create.
 
-		if daemonClient != nil {
-			resp, err := daemonClient.List(&rpc.ListArgs{})
+Formulas are ephemeral proto definitions stored as .formula.json files.
+They are cooked inline when pouring, never stored as database beads.
+
+Search paths (in priority order):
+  1. .beads/formulas/       (project-level)
+  2. ~/.beads/formulas/     (user-level)
+  3. ~/gt/.beads/formulas/  (Gas Town level)`,
+	Run: func(cmd *cobra.Command, args []string) {
+		typeFilter, _ := cmd.Flags().GetString("type")
+
+		// Get all search paths and scan for formulas
+		searchPaths := getFormulaSearchPaths()
+		seen := make(map[string]bool)
+		var entries []CatalogEntry
+
+		for _, dir := range searchPaths {
+			formulas, err := scanFormulaDir(dir)
 			if err != nil {
-				fmt.Fprintf(os.Stderr, "Error loading molecules: %v\n", err)
-				os.Exit(1)
+				continue // Skip inaccessible directories
 			}
-			var allIssues []*types.Issue
-			if err := json.Unmarshal(resp.Data, &allIssues); err == nil {
-				for _, issue := range allIssues {
-					for _, label := range issue.Labels {
-						if label == MoleculeLabel {
-							molecules = append(molecules, issue)
-							break
-						}
-					}
+
+			for _, f := range formulas {
+				if seen[f.Formula] {
+					continue // Skip shadowed formulas
 				}
+				seen[f.Formula] = true
+
+				// Apply type filter
+				if typeFilter != "" && string(f.Type) != typeFilter {
+					continue
+				}
+
+				// Extract variable names
+				var varNames []string
+				for name := range f.Vars {
+					varNames = append(varNames, name)
+				}
+				sort.Strings(varNames)
+
+				entries = append(entries, CatalogEntry{
+					Name:        f.Formula,
+					Type:        string(f.Type),
+					Description: truncateDescription(f.Description, 60),
+					Source:      f.Source,
+					Steps:       countSteps(f.Steps),
+					Vars:        varNames,
+				})
 			}
-		} else if store != nil {
-			var err error
-			molecules, err = store.GetIssuesByLabel(ctx, MoleculeLabel)
-			if err != nil {
-				fmt.Fprintf(os.Stderr, "Error loading molecules: %v\n", err)
-				os.Exit(1)
-			}
-		} else {
-			fmt.Fprintf(os.Stderr, "Error: no database connection\n")
-			os.Exit(1)
 		}
 
+		// Sort by name
+		sort.Slice(entries, func(i, j int) bool {
+			return entries[i].Name < entries[j].Name
+		})
+
 		if jsonOutput {
-			outputJSON(molecules)
+			outputJSON(entries)
 			return
 		}
 
-		if len(molecules) == 0 {
-			fmt.Println("No protos available.")
-			fmt.Println("\nTo create a proto:")
-			fmt.Println("  1. Create an epic with child issues")
-			fmt.Println("  2. Add the 'template' label: bd label add <epic-id> template")
-			fmt.Println("  3. Use {{variable}} placeholders in titles/descriptions")
-			fmt.Println("\nTo instantiate a molecule from a proto:")
-			fmt.Println("  bd pour <id> --var key=value          # persistent mol")
-			fmt.Println("  bd wisp create <id> --var key=value   # ephemeral wisp")
+		if len(entries) == 0 {
+			fmt.Println("No formulas found.")
+			fmt.Println("\nTo create a formula, write a .formula.json file:")
+			fmt.Println("  .beads/formulas/my-workflow.formula.json")
+			fmt.Println("\nOr distill from existing work:")
+			fmt.Println("  bd mol distill <epic-id> my-workflow")
+			fmt.Println("\nTo instantiate from formula:")
+			fmt.Println("  bd pour <formula-name> --var key=value          # persistent mol")
+			fmt.Println("  bd wisp create <formula-name> --var key=value   # ephemeral wisp")
 			return
 		}
 
-		fmt.Printf("%s\n", ui.RenderPass("Protos (for bd pour / bd wisp create):"))
-		for _, mol := range molecules {
-			vars := extractVariables(mol.Title + " " + mol.Description)
-			varStr := ""
-			if len(vars) > 0 {
-				varStr = fmt.Sprintf(" (vars: %s)", strings.Join(vars, ", "))
+		fmt.Printf("%s\n\n", ui.RenderPass("Formulas (for bd pour / bd wisp create):"))
+
+		// Group by type for display
+		byType := make(map[string][]CatalogEntry)
+		for _, e := range entries {
+			byType[e.Type] = append(byType[e.Type], e)
+		}
+
+		// Print workflow types first (most common for pour/wisp)
+		typeOrder := []string{"workflow", "expansion", "aspect"}
+		for _, t := range typeOrder {
+			typeEntries := byType[t]
+			if len(typeEntries) == 0 {
+				continue
 			}
-			fmt.Printf("  %s: %s%s\n", ui.RenderAccent(mol.ID), mol.Title, varStr)
+
+			typeIcon := getTypeIcon(t)
+			fmt.Printf("%s %s:\n", typeIcon, strings.Title(t))
+
+			for _, e := range typeEntries {
+				varInfo := ""
+				if len(e.Vars) > 0 {
+					varInfo = fmt.Sprintf(" (vars: %s)", strings.Join(e.Vars, ", "))
+				}
+				fmt.Printf("  %s: %s%s\n", ui.RenderAccent(e.Name), e.Description, varInfo)
+			}
+			fmt.Println()
 		}
-		fmt.Println()
 	},
 }
 
 func init() {
+	molCatalogCmd.Flags().String("type", "", "Filter by formula type (workflow, expansion, aspect)")
 	molCmd.AddCommand(molCatalogCmd)
 }

cmd/bd/mol_distill.go

@@ -1,28 +1,29 @@
 package main
 
 import (
-	"context"
+	"encoding/json"
 	"fmt"
 	"os"
+	"path/filepath"
+	"regexp"
 	"strings"
 
 	"github.com/spf13/cobra"
-	"github.com/steveyegge/beads/internal/storage"
-	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/formula"
 	"github.com/steveyegge/beads/internal/ui"
 	"github.com/steveyegge/beads/internal/utils"
 )
 
 var molDistillCmd = &cobra.Command{
-	Use:   "distill <epic-id>",
-	Short: "Extract a reusable proto from an existing epic",
-	Long: `Distill a molecule by extracting a reusable proto from an existing epic.
+	Use:   "distill <epic-id> [formula-name]",
+	Short: "Extract a formula from an existing epic",
+	Long: `Distill a molecule by extracting a reusable formula from an existing epic.
 
-This is the reverse of spawn: instead of proto → molecule, it's molecule → proto.
+This is the reverse of pour: instead of formula → molecule, it's molecule → formula.
 
 The distill command:
   1. Loads the existing epic and all its children
-  2. Clones the structure as a new proto (adds "template" label)
+  2. Converts the structure to a .formula.json file
   3. Replaces concrete values with {{variable}} placeholders (via --var flags)
 
 Use cases:
@@ -34,19 +35,23 @@ Variable syntax (both work - we detect which side is the concrete value):
   --var branch=feature-auth    Spawn-style: variable=value (recommended)
   --var feature-auth=branch    Substitution-style: value=variable
 
+Output locations (first writable wins):
+  1. .beads/formulas/       (project-level, default)
+  2. ~/.beads/formulas/     (user-level, if project not writable)
+
 Examples:
-  bd mol distill bd-o5xe --as "Release Workflow"
-  bd mol distill bd-abc --var feature_name=auth-refactor --var version=1.0.0`,
-	Args: cobra.ExactArgs(1),
+  bd mol distill bd-o5xe my-workflow
+  bd mol distill bd-abc release-workflow --var feature_name=auth-refactor`,
+	Args: cobra.RangeArgs(1, 2),
 	Run:  runMolDistill,
 }
 
 // DistillResult holds the result of a distill operation
 type DistillResult struct {
-	ProtoID   string            `json:"proto_id"`
-	IDMapping map[string]string `json:"id_mapping"` // old ID -> new ID
-	Created   int               `json:"created"`    // number of issues created
-	Variables []string          `json:"variables"`  // variables introduced
+	FormulaName string   `json:"formula_name"`
+	FormulaPath string   `json:"formula_path"`
+	Steps       int      `json:"steps"`     // number of steps in formula
+	Variables   []string `json:"variables"` // variables introduced
 }
 
 // collectSubgraphText gathers all searchable text from a molecule subgraph
@@ -95,11 +100,9 @@ func parseDistillVar(varFlag, searchableText string) (string, string, error) {
 
 // runMolDistill implements the distill command
 func runMolDistill(cmd *cobra.Command, args []string) {
-	CheckReadonly("mol distill")
-
 	ctx := rootCtx
 
-	// mol distill requires direct store access
+	// mol distill requires direct store access for reading the epic
 	if store == nil {
 		if daemonClient != nil {
 			fmt.Fprintf(os.Stderr, "Error: mol distill requires direct database access\n")
@@ -110,9 +113,9 @@ func runMolDistill(cmd *cobra.Command, args []string) {
 		os.Exit(1)
 	}
 
-	customTitle, _ := cmd.Flags().GetString("as")
 	varFlags, _ := cmd.Flags().GetStringSlice("var")
 	dryRun, _ := cmd.Flags().GetBool("dry-run")
+	outputDir, _ := cmd.Flags().GetString("output")
 
 	// Resolve epic ID
 	epicID, err := utils.ResolvePartialID(ctx, store, args[0])
@@ -121,15 +124,23 @@ func runMolDistill(cmd *cobra.Command, args []string) {
 		os.Exit(1)
 	}
 
-	// Load the epic subgraph (needed for smart var detection)
+	// Load the epic subgraph
 	subgraph, err := loadTemplateSubgraph(ctx, store, epicID)
 	if err != nil {
 		fmt.Fprintf(os.Stderr, "Error loading epic: %v\n", err)
 		os.Exit(1)
 	}
 
+	// Determine formula name
+	formulaName := ""
+	if len(args) > 1 {
+		formulaName = args[1]
+	} else {
+		// Derive from epic title
+		formulaName = sanitizeFormulaName(subgraph.Root.Title)
+	}
+
 	// Parse variable substitutions with smart detection
-	// Accepts both spawn-style (variable=value) and substitution-style (value=variable)
 	replacements := make(map[string]string)
 	if len(varFlags) > 0 {
 		searchableText := collectSubgraphText(subgraph)
@@ -143,76 +154,127 @@ func runMolDistill(cmd *cobra.Command, args []string) {
 		}
 	}
 
-	if dryRun {
-		fmt.Printf("\nDry run: would distill %d issues from %s into a proto\n\n", len(subgraph.Issues), epicID)
-		fmt.Printf("Source: %s\n", subgraph.Root.Title)
-		if customTitle != "" {
-			fmt.Printf("Proto title: %s\n", customTitle)
+	// Convert to formula
+	f := subgraphToFormula(subgraph, formulaName, replacements)
+
+	// Determine output path
+	outputPath := ""
+	if outputDir != "" {
+		outputPath = filepath.Join(outputDir, formulaName+formula.FormulaExt)
+	} else {
+		// Find first writable formula directory
+		outputPath = findWritableFormulaDir(formulaName)
+		if outputPath == "" {
+			fmt.Fprintf(os.Stderr, "Error: no writable formula directory found\n")
+			fmt.Fprintf(os.Stderr, "Try: mkdir -p .beads/formulas\n")
+			os.Exit(1)
 		}
+	}
+
+	if dryRun {
+		fmt.Printf("\nDry run: would distill %d steps from %s into formula\n\n", countSteps(f.Steps), epicID)
+		fmt.Printf("Formula: %s\n", formulaName)
+		fmt.Printf("Output: %s\n", outputPath)
 		if len(replacements) > 0 {
-			fmt.Printf("\nVariable substitutions:\n")
+			fmt.Printf("\nVariables:\n")
 			for value, varName := range replacements {
-				fmt.Printf("  \"%s\" → {{%s}}\n", value, varName)
+				fmt.Printf("  %s: \"%s\" → {{%s}}\n", varName, value, varName)
 			}
 		}
 		fmt.Printf("\nStructure:\n")
-		for _, issue := range subgraph.Issues {
-			title := issue.Title
-			for value, varName := range replacements {
-				title = strings.ReplaceAll(title, value, "{{"+varName+"}}")
-			}
-			prefix := "  "
-			if issue.ID == subgraph.Root.ID {
-				prefix = "→ "
-			}
-			fmt.Printf("%s%s\n", prefix, title)
-		}
+		printFormulaStepsTree(f.Steps, "")
 		return
 	}
 
-	// Distill the molecule into a proto
-	result, err := distillMolecule(ctx, store, subgraph, customTitle, replacements, actor)
-	if err != nil {
-		fmt.Fprintf(os.Stderr, "Error distilling molecule: %v\n", err)
+	// Ensure output directory exists
+	dir := filepath.Dir(outputPath)
+	if err := os.MkdirAll(dir, 0755); err != nil {
+		fmt.Fprintf(os.Stderr, "Error creating directory %s: %v\n", dir, err)
 		os.Exit(1)
 	}
 
-	// Schedule auto-flush
-	markDirtyAndScheduleFlush()
+	// Write formula
+	data, err := json.MarshalIndent(f, "", "  ")
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error encoding formula: %v\n", err)
+		os.Exit(1)
+	}
+
+	// #nosec G306 -- Formula files are not sensitive
+	if err := os.WriteFile(outputPath, data, 0644); err != nil {
+		fmt.Fprintf(os.Stderr, "Error writing formula: %v\n", err)
+		os.Exit(1)
+	}
+
+	result := &DistillResult{
+		FormulaName: formulaName,
+		FormulaPath: outputPath,
+		Steps:       countSteps(f.Steps),
+		Variables:   getVarNames(replacements),
+	}
 
 	if jsonOutput {
 		outputJSON(result)
 		return
 	}
 
-	fmt.Printf("%s Distilled proto: created %d issues\n", ui.RenderPass("✓"), result.Created)
-	fmt.Printf("  Proto ID: %s\n", result.ProtoID)
+	fmt.Printf("%s Distilled formula: %d steps\n", ui.RenderPass("✓"), result.Steps)
+	fmt.Printf("  Formula: %s\n", result.FormulaName)
+	fmt.Printf("  Path: %s\n", result.FormulaPath)
 	if len(result.Variables) > 0 {
 		fmt.Printf("  Variables: %s\n", strings.Join(result.Variables, ", "))
 	}
-	fmt.Printf("\nTo instantiate this proto:\n")
-	fmt.Printf("  bd pour %s", result.ProtoID[:8])
+	fmt.Printf("\nTo instantiate:\n")
+	fmt.Printf("  bd pour %s", result.FormulaName)
 	for _, v := range result.Variables {
 		fmt.Printf(" --var %s=<value>", v)
 	}
 	fmt.Println()
 }
 
-// distillMolecule creates a new proto from an existing epic
-func distillMolecule(ctx context.Context, s storage.Storage, subgraph *MoleculeSubgraph, customTitle string, replacements map[string]string, actorName string) (*DistillResult, error) {
-	if s == nil {
-		return nil, fmt.Errorf("no database connection")
+// sanitizeFormulaName converts a title to a valid formula name
+func sanitizeFormulaName(title string) string {
+	// Convert to lowercase and replace spaces/special chars with hyphens
+	re := regexp.MustCompile(`[^a-zA-Z0-9-]+`)
+	name := re.ReplaceAllString(strings.ToLower(title), "-")
+	// Remove leading/trailing hyphens and collapse multiple hyphens
+	name = regexp.MustCompile(`-+`).ReplaceAllString(name, "-")
+	name = strings.Trim(name, "-")
+	if name == "" {
+		name = "untitled"
 	}
+	return name
+}
 
-	// Build the reverse mapping for tracking variables introduced
-	var variables []string
+// findWritableFormulaDir finds the first writable formula directory
+func findWritableFormulaDir(formulaName string) string {
+	searchPaths := getFormulaSearchPaths()
+	for _, dir := range searchPaths {
+		// Try to create the directory if it doesn't exist
+		if err := os.MkdirAll(dir, 0755); err == nil {
+			// Check if we can write to it
+			testPath := filepath.Join(dir, ".write-test")
+			if f, err := os.Create(testPath); err == nil {
+				f.Close()
+				os.Remove(testPath)
+				return filepath.Join(dir, formulaName+formula.FormulaExt)
+			}
+		}
+	}
+	return ""
+}
+
+// getVarNames extracts variable names from replacements map
+func getVarNames(replacements map[string]string) []string {
+	var names []string
 	for _, varName := range replacements {
-		variables = append(variables, varName)
+		names = append(names, varName)
 	}
+	return names
+}
 
-	// Generate new IDs and create mapping
-	idMapping := make(map[string]string)
-
+// subgraphToFormula converts a molecule subgraph to a formula
+func subgraphToFormula(subgraph *TemplateSubgraph, name string, replacements map[string]string) *formula.Formula {
 	// Helper to apply replacements
 	applyReplacements := func(text string) string {
 		result := text
@@ -222,87 +284,88 @@ func distillMolecule(ctx context.Context, s storage.Storage, subgraph *MoleculeS
 		return result
 	}
 
-	// Use transaction for atomicity
-	err := s.RunInTransaction(ctx, func(tx storage.Transaction) error {
-		// First pass: create all issues with new IDs
-		for _, oldIssue := range subgraph.Issues {
-			// Determine title
-			title := applyReplacements(oldIssue.Title)
-			if oldIssue.ID == subgraph.Root.ID && customTitle != "" {
-				title = customTitle
-			}
-
-			// Add template label to all issues
-			labels := append([]string{}, oldIssue.Labels...)
-			hasTemplateLabel := false
-			for _, l := range labels {
-				if l == MoleculeLabel {
-					hasTemplateLabel = true
-					break
-				}
-			}
-			if !hasTemplateLabel {
-				labels = append(labels, MoleculeLabel)
-			}
-
-			newIssue := &types.Issue{
-				Title:              title,
-				Description:        applyReplacements(oldIssue.Description),
-				Design:             applyReplacements(oldIssue.Design),
-				AcceptanceCriteria: applyReplacements(oldIssue.AcceptanceCriteria),
-				Notes:              applyReplacements(oldIssue.Notes),
-				Status:             types.StatusOpen, // Protos start fresh
-				Priority:           oldIssue.Priority,
-				IssueType:          oldIssue.IssueType,
-				Labels:             labels,
-				EstimatedMinutes:   oldIssue.EstimatedMinutes,
-				IDPrefix:           "proto", // bd-hobo: distinct prefix for protos
-			}
-
-			if err := tx.CreateIssue(ctx, newIssue, actorName); err != nil {
-				return fmt.Errorf("failed to create proto issue from %s: %w", oldIssue.ID, err)
-			}
-
-			idMapping[oldIssue.ID] = newIssue.ID
+	// Build ID mapping for step references
+	idToStepID := make(map[string]string)
+	for _, issue := range subgraph.Issues {
+		// Create a sanitized step ID from the issue ID
+		stepID := sanitizeFormulaName(issue.Title)
+		if stepID == "" {
+			stepID = issue.ID
 		}
-
-		// Second pass: recreate dependencies with new IDs
-		for _, dep := range subgraph.Dependencies {
-			newFromID, ok1 := idMapping[dep.IssueID]
-			newToID, ok2 := idMapping[dep.DependsOnID]
-			if !ok1 || !ok2 {
-				continue // Skip if either end is outside the subgraph
-			}
-
-			newDep := &types.Dependency{
-				IssueID:     newFromID,
-				DependsOnID: newToID,
-				Type:        dep.Type,
-			}
-			if err := tx.AddDependency(ctx, newDep, actorName); err != nil {
-				return fmt.Errorf("failed to create dependency: %w", err)
-			}
-		}
-
-		return nil
-	})
-
-	if err != nil {
-		return nil, err
+		idToStepID[issue.ID] = stepID
 	}
 
-	return &DistillResult{
-		ProtoID:   idMapping[subgraph.Root.ID],
-		IDMapping: idMapping,
-		Created:   len(subgraph.Issues),
-		Variables: variables,
-	}, nil
+	// Build dependency map (issue ID -> list of depends-on IDs)
+	depsByIssue := make(map[string][]string)
+	for _, dep := range subgraph.Dependencies {
+		depsByIssue[dep.IssueID] = append(depsByIssue[dep.IssueID], dep.DependsOnID)
+	}
+
+	// Convert issues to steps
+	var steps []*formula.Step
+	for _, issue := range subgraph.Issues {
+		if issue.ID == subgraph.Root.ID {
+			continue // Root becomes the formula itself
+		}
+
+		step := &formula.Step{
+			ID:          idToStepID[issue.ID],
+			Title:       applyReplacements(issue.Title),
+			Description: applyReplacements(issue.Description),
+			Type:        string(issue.IssueType),
+		}
+
+		// Copy priority if set
+		if issue.Priority > 0 {
+			p := issue.Priority
+			step.Priority = &p
+		}
+
+		// Copy labels (excluding internal ones)
+		for _, label := range issue.Labels {
+			if label != MoleculeLabel && !strings.HasPrefix(label, "mol:") {
+				step.Labels = append(step.Labels, label)
+			}
+		}
+
+		// Convert dependencies to depends_on (skip root)
+		if deps, ok := depsByIssue[issue.ID]; ok {
+			for _, depID := range deps {
+				if depID == subgraph.Root.ID {
+					continue // Skip dependency on root (becomes formula itself)
+				}
+				if stepID, ok := idToStepID[depID]; ok {
+					step.DependsOn = append(step.DependsOn, stepID)
+				}
+			}
+		}
+
+		steps = append(steps, step)
+	}
+
+	// Build variable definitions
+	vars := make(map[string]*formula.VarDef)
+	for _, varName := range replacements {
+		vars[varName] = &formula.VarDef{
+			Description: fmt.Sprintf("Value for %s", varName),
+			Required:    true,
+		}
+	}
+
+	return &formula.Formula{
+		Formula:     name,
+		Description: applyReplacements(subgraph.Root.Description),
+		Version:     1,
+		Type:        formula.TypeWorkflow,
+		Vars:        vars,
+		Steps:       steps,
+	}
 }
 
 func init() {
-	molDistillCmd.Flags().String("as", "", "Custom title for the new proto")
-	molDistillCmd.Flags().StringSlice("var", []string{}, "Replace value with {{variable}} placeholder (value=variable)")
+	molDistillCmd.Flags().StringSlice("var", []string{}, "Replace value with {{variable}} placeholder (variable=value)")
 	molDistillCmd.Flags().Bool("dry-run", false, "Preview what would be created")
+	molDistillCmd.Flags().String("output", "", "Output directory for formula file")
 
 	molCmd.AddCommand(molDistillCmd)
 }

cmd/bd/pour.go

@@ -17,7 +17,7 @@ import (
 //   - Proto (solid) -> pour -> Mol (liquid)
 //   - Pour creates persistent, auditable work in .beads/
 var pourCmd = &cobra.Command{
-	Use:   "pour <proto-id-or-formula>",
+	Use:   "pour <proto-id>",
 	Short: "Instantiate a proto as a persistent mol (solid -> liquid)",
 	Long: `Pour a proto into a persistent mol - like pouring molten metal into a mold.
 
@@ -26,20 +26,13 @@ The resulting mol lives in .beads/ (permanent storage) and is synced with git.
 
 Phase transition: Proto (solid) -> pour -> Mol (liquid)
 
-The argument can be:
-  - A proto ID (existing proto in database): bd pour mol-feature
-  - A formula name (cooked inline): bd pour mol-feature --var name=auth
-
-When given a formula name, pour cooks it inline as an ephemeral proto,
-spawns the mol, then cleans up the temporary proto (bd-rciw).
-
 Use pour for:
   - Feature work that spans sessions
   - Important work needing audit trail
   - Anything you might need to reference later
 
 Examples:
-  bd pour mol-feature --var name=auth    # Formula cooked inline
+  bd pour mol-feature --var name=auth    # Create persistent mol from proto
   bd pour mol-release --var version=1.0  # Release workflow
   bd pour mol-review --var pr=123        # Code review workflow`,
 	Args: cobra.ExactArgs(1),
@@ -51,7 +44,7 @@ func runPour(cmd *cobra.Command, args []string) {
 
 	ctx := rootCtx
 
-	// Pour requires direct store access for subgraph loading and cloning
+	// Pour requires direct store access for cloning
 	if store == nil {
 		if daemonClient != nil {
 			fmt.Fprintf(os.Stderr, "Error: pour requires direct database access\n")
@@ -79,68 +72,75 @@ func runPour(cmd *cobra.Command, args []string) {
 		vars[parts[0]] = parts[1]
 	}
 
-	// Resolve proto ID or cook formula inline (bd-rciw)
-	// This accepts either:
-	// - An existing proto ID: bd pour mol-feature
-	// - A formula name: bd pour mol-feature (cooked inline as ephemeral proto)
-	protoIssue, cookedProto, err := resolveOrCookFormula(ctx, store, args[0], actor)
-	if err != nil {
-		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
-		os.Exit(1)
+	// Try to load as formula first (ephemeral proto - gt-4v1eo)
+	// If that fails, fall back to loading from DB (legacy proto beads)
+	var subgraph *TemplateSubgraph
+	var protoID string
+	isFormula := false
+
+	// Try to cook formula inline (gt-4v1eo: ephemeral protos)
+	// This works for any valid formula name, not just "mol-" prefixed ones
+	sg, err := resolveAndCookFormula(args[0], nil)
+	if err == nil {
+		subgraph = sg
+		protoID = sg.Root.ID
+		isFormula = true
 	}
 
-	// Track cooked formula for cleanup
-	cleanupCooked := func() {
-		if cookedProto {
-			_ = deleteProtoSubgraph(ctx, store, protoIssue.ID)
+	if subgraph == nil {
+		// Try to load as existing proto bead (legacy path)
+		resolvedID, err := utils.ResolvePartialID(ctx, store, args[0])
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error: %s not found as formula or proto ID\n", args[0])
+			os.Exit(1)
+		}
+		protoID = resolvedID
+
+		// Verify it's a proto
+		protoIssue, err := store.GetIssue(ctx, protoID)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error loading proto %s: %v\n", protoID, err)
+			os.Exit(1)
+		}
+		if !isProto(protoIssue) {
+			fmt.Fprintf(os.Stderr, "Error: %s is not a proto (missing '%s' label)\n", protoID, MoleculeLabel)
+			os.Exit(1)
+		}
+
+		// Load the proto subgraph from DB
+		subgraph, err = loadTemplateSubgraph(ctx, store, protoID)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error loading proto: %v\n", err)
+			os.Exit(1)
 		}
 	}
 
-	protoID := protoIssue.ID
-
-	// Verify it's a proto
-	if !isProto(protoIssue) {
-		cleanupCooked()
-		fmt.Fprintf(os.Stderr, "Error: %s is not a proto (missing '%s' label)\n", protoID, MoleculeLabel)
-		os.Exit(1)
-	}
-
-	// Load the proto subgraph
-	subgraph, err := loadTemplateSubgraph(ctx, store, protoID)
-	if err != nil {
-		cleanupCooked()
-		fmt.Fprintf(os.Stderr, "Error loading proto: %v\n", err)
-		os.Exit(1)
-	}
+	_ = isFormula // For future use (e.g., logging)
 
 	// Resolve and load attached protos
 	type attachmentInfo struct {
 		id       string
 		issue    *types.Issue
-		subgraph *MoleculeSubgraph
+		subgraph *TemplateSubgraph
 	}
 	var attachments []attachmentInfo
 	for _, attachArg := range attachFlags {
 		attachID, err := utils.ResolvePartialID(ctx, store, attachArg)
 		if err != nil {
-			cleanupCooked()
 			fmt.Fprintf(os.Stderr, "Error resolving attachment ID %s: %v\n", attachArg, err)
 			os.Exit(1)
 		}
 		attachIssue, err := store.GetIssue(ctx, attachID)
 		if err != nil {
-			cleanupCooked()
 			fmt.Fprintf(os.Stderr, "Error loading attachment %s: %v\n", attachID, err)
 			os.Exit(1)
 		}
 		if !isProto(attachIssue) {
-			cleanupCooked()
 			fmt.Fprintf(os.Stderr, "Error: %s is not a proto (missing '%s' label)\n", attachID, MoleculeLabel)
 			os.Exit(1)
 		}
 		attachSubgraph, err := loadTemplateSubgraph(ctx, store, attachID)
 		if err != nil {
-			cleanupCooked()
 			fmt.Fprintf(os.Stderr, "Error loading attachment subgraph %s: %v\n", attachID, err)
 			os.Exit(1)
 		}
@@ -151,10 +151,13 @@ func runPour(cmd *cobra.Command, args []string) {
 		})
 	}
 
-	// Check for missing variables
-	requiredVars := extractAllVariables(subgraph)
+	// Apply variable defaults from formula (gt-4v1eo)
+	vars = applyVariableDefaults(vars, subgraph)
+
+	// Check for missing required variables (those without defaults)
+	requiredVars := extractRequiredVariables(subgraph)
 	for _, attach := range attachments {
-		attachVars := extractAllVariables(attach.subgraph)
+		attachVars := extractRequiredVariables(attach.subgraph)
 		for _, v := range attachVars {
 			found := false
 			for _, rv := range requiredVars {
@@ -175,7 +178,6 @@ func runPour(cmd *cobra.Command, args []string) {
 		}
 	}
 	if len(missingVars) > 0 {
-		cleanupCooked()
 		fmt.Fprintf(os.Stderr, "Error: missing required variables: %s\n", strings.Join(missingVars, ", "))
 		fmt.Fprintf(os.Stderr, "Provide them with: --var %s=<value>\n", missingVars[0])
 		os.Exit(1)
@@ -198,10 +200,6 @@ func runPour(cmd *cobra.Command, args []string) {
 				fmt.Printf("  + %s (%d issues)\n", attach.issue.Title, len(attach.subgraph.Issues))
 			}
 		}
-		if cookedProto {
-			fmt.Printf("\n  Note: Formula cooked inline as ephemeral proto.\n")
-		}
-		cleanupCooked()
 		return
 	}
 
@@ -209,7 +207,6 @@ func runPour(cmd *cobra.Command, args []string) {
 	// bd-hobo: Use "mol" prefix for distinct visual recognition
 	result, err := spawnMolecule(ctx, store, subgraph, vars, assignee, actor, false, "mol")
 	if err != nil {
-		cleanupCooked()
 		fmt.Fprintf(os.Stderr, "Error pouring proto: %v\n", err)
 		os.Exit(1)
 	}
@@ -219,7 +216,6 @@ func runPour(cmd *cobra.Command, args []string) {
 	if len(attachments) > 0 {
 		spawnedMol, err := store.GetIssue(ctx, result.NewEpicID)
 		if err != nil {
-			cleanupCooked()
 			fmt.Fprintf(os.Stderr, "Error loading spawned mol: %v\n", err)
 			os.Exit(1)
 		}
@@ -228,7 +224,6 @@ func runPour(cmd *cobra.Command, args []string) {
 			// pour command always creates persistent (Wisp=false) issues
 			bondResult, err := bondProtoMol(ctx, store, attach.issue, spawnedMol, attachType, vars, "", actor, false, true)
 			if err != nil {
-				cleanupCooked()
 				fmt.Fprintf(os.Stderr, "Error attaching %s: %v\n", attach.id, err)
 				os.Exit(1)
 			}
@@ -236,20 +231,16 @@ func runPour(cmd *cobra.Command, args []string) {
 		}
 	}
 
-	// Clean up ephemeral proto after successful spawn (bd-rciw)
-	cleanupCooked()
-
 	// Schedule auto-flush
 	markDirtyAndScheduleFlush()
 
 	if jsonOutput {
 		type pourResult struct {
 			*InstantiateResult
-			Attached     int    `json:"attached"`
-			Phase        string `json:"phase"`
-			CookedInline bool   `json:"cooked_inline,omitempty"`
+			Attached int    `json:"attached"`
+			Phase    string `json:"phase"`
 		}
-		outputJSON(pourResult{result, totalAttached, "liquid", cookedProto})
+		outputJSON(pourResult{result, totalAttached, "liquid"})
 		return
 	}
 
@@ -259,9 +250,6 @@ func runPour(cmd *cobra.Command, args []string) {
 	if totalAttached > 0 {
 		fmt.Printf("  Attached: %d issues from %d protos\n", totalAttached, len(attachments))
 	}
-	if cookedProto {
-		fmt.Printf("  Ephemeral proto cleaned up after use.\n")
-	}
 }
 
 func init() {

cmd/bd/template.go

@@ -10,6 +10,7 @@ import (
 	"time"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/formula"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/types"
@@ -25,10 +26,11 @@ var variablePattern = regexp.MustCompile(`\{\{([a-zA-Z_][a-zA-Z0-9_]*)\}\}`)
 
 // TemplateSubgraph holds a template epic and all its descendants
 type TemplateSubgraph struct {
-	Root         *types.Issue            // The template epic
-	Issues       []*types.Issue          // All issues in the subgraph (including root)
-	Dependencies []*types.Dependency     // All dependencies within the subgraph
-	IssueMap     map[string]*types.Issue // ID -> Issue for quick lookup
+	Root         *types.Issue                // The template epic
+	Issues       []*types.Issue              // All issues in the subgraph (including root)
+	Dependencies []*types.Dependency         // All dependencies within the subgraph
+	IssueMap     map[string]*types.Issue     // ID -> Issue for quick lookup
+	VarDefs      map[string]formula.VarDef   // Variable definitions from formula (for defaults)
 }
 
 // InstantiateResult holds the result of template instantiation
@@ -787,6 +789,57 @@ func extractAllVariables(subgraph *TemplateSubgraph) []string {
 	return extractVariables(allText)
 }
 
+// extractRequiredVariables returns only variables that don't have defaults.
+// If VarDefs is available (from a cooked formula), uses it to filter out defaulted vars.
+// Otherwise, falls back to returning all variables.
+func extractRequiredVariables(subgraph *TemplateSubgraph) []string {
+	allVars := extractAllVariables(subgraph)
+
+	// If no VarDefs, assume all variables are required
+	if subgraph.VarDefs == nil || len(subgraph.VarDefs) == 0 {
+		return allVars
+	}
+
+	// Filter to only required variables (no default and marked as required, or not defined in VarDefs)
+	var required []string
+	for _, v := range allVars {
+		def, exists := subgraph.VarDefs[v]
+		// A variable is required if:
+		// 1. It's not defined in VarDefs at all, OR
+		// 2. It's defined with Required=true and no Default, OR
+		// 3. It's defined with no Default (even if Required is false)
+		if !exists {
+			required = append(required, v)
+		} else if def.Default == "" {
+			required = append(required, v)
+		}
+		// If exists and has default, it's not required
+	}
+	return required
+}
+
+// applyVariableDefaults merges formula default values with provided variables.
+// Returns a new map with defaults applied for any missing variables.
+func applyVariableDefaults(vars map[string]string, subgraph *TemplateSubgraph) map[string]string {
+	if subgraph.VarDefs == nil {
+		return vars
+	}
+
+	result := make(map[string]string)
+	for k, v := range vars {
+		result[k] = v
+	}
+
+	// Apply defaults for missing variables
+	for name, def := range subgraph.VarDefs {
+		if _, exists := result[name]; !exists && def.Default != "" {
+			result[name] = def.Default
+		}
+	}
+
+	return result
+}
+
 // substituteVariables replaces {{variable}} with values
 func substituteVariables(text string, vars map[string]string) string {
 	return variablePattern.ReplaceAllStringFunc(text, func(match string) string {

cmd/bd/wisp.go

@@ -1,6 +1,7 @@
 package main
 
 import (
+	"context"
 	"encoding/json"
 	"fmt"
 	"os"
@@ -69,7 +70,7 @@ const OldThreshold = 24 * time.Hour
 
 // wispCreateCmd instantiates a proto as an ephemeral wisp
 var wispCreateCmd = &cobra.Command{
-	Use:   "create <proto-id-or-formula>",
+	Use:   "create <proto-id>",
 	Short: "Instantiate a proto as an ephemeral wisp (solid -> vapor)",
 	Long: `Create a wisp from a proto - sublimation from solid to vapor.
 
@@ -78,13 +79,6 @@ The resulting wisp is stored in the main database with Wisp=true and NOT exporte
 
 Phase transition: Proto (solid) -> Wisp (vapor)
 
-The argument can be:
-  - A proto ID (existing proto in database): bd wisp create mol-patrol
-  - A formula name (cooked inline): bd wisp create mol-patrol --var name=ace
-
-When given a formula name, wisp cooks it inline as an ephemeral proto,
-creates the wisp, then cleans up the temporary proto (bd-rciw).
-
 Use wisp create for:
   - Patrol cycles (deacon, witness)
   - Health checks and monitoring
@@ -97,8 +91,8 @@ The wisp will:
   - Either evaporate (burn) or condense to digest (squash)
 
 Examples:
-  bd wisp create mol-patrol                       # Formula cooked inline
-  bd wisp create mol-health-check                 # One-time health check
+  bd wisp create mol-patrol                    # Ephemeral patrol cycle
+  bd wisp create mol-health-check              # One-time health check
   bd wisp create mol-diagnostics --var target=db  # Diagnostic run`,
 	Args: cobra.ExactArgs(1),
 	Run:  runWispCreate,
@@ -134,42 +128,79 @@ func runWispCreate(cmd *cobra.Command, args []string) {
 		vars[parts[0]] = parts[1]
 	}
 
-	// Resolve proto ID or cook formula inline (bd-rciw)
-	// This accepts either:
-	// - An existing proto ID: bd wisp create mol-patrol
-	// - A formula name: bd wisp create mol-patrol (cooked inline as ephemeral proto)
-	protoIssue, cookedProto, err := resolveOrCookFormula(ctx, store, args[0], actor)
-	if err != nil {
-		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
-		os.Exit(1)
+	// Try to load as formula first (ephemeral proto - gt-4v1eo)
+	// If that fails, fall back to loading from DB (legacy proto beads)
+	var subgraph *TemplateSubgraph
+	var protoID string
+
+	// Try to cook formula inline (gt-4v1eo: ephemeral protos)
+	// This works for any valid formula name, not just "mol-" prefixed ones
+	sg, err := resolveAndCookFormula(args[0], nil)
+	if err == nil {
+		subgraph = sg
+		protoID = sg.Root.ID
 	}
 
-	// Track cooked formula for cleanup
-	cleanupCooked := func() {
-		if cookedProto {
-			_ = deleteProtoSubgraph(ctx, store, protoIssue.ID)
+	if subgraph == nil {
+		// Resolve proto ID (legacy path)
+		protoID = args[0]
+		// Try to resolve partial ID if it doesn't look like a full ID
+		if !strings.HasPrefix(protoID, "bd-") && !strings.HasPrefix(protoID, "gt-") && !strings.HasPrefix(protoID, "mol-") {
+			// Might be a partial ID, try to resolve
+			if resolved, err := resolvePartialIDDirect(ctx, protoID); err == nil {
+				protoID = resolved
+			}
+		}
+
+		// Check if it's a named molecule (mol-xxx) - look up in catalog
+		if strings.HasPrefix(protoID, "mol-") {
+			// Find the proto by name
+			issues, err := store.SearchIssues(ctx, "", types.IssueFilter{
+				Labels: []string{MoleculeLabel},
+			})
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error searching for proto: %v\n", err)
+				os.Exit(1)
+			}
+			found := false
+			for _, issue := range issues {
+				if strings.Contains(issue.Title, protoID) || issue.ID == protoID {
+					protoID = issue.ID
+					found = true
+					break
+				}
+			}
+			if !found {
+				fmt.Fprintf(os.Stderr, "Error: '%s' not found as formula or proto\n", args[0])
+				fmt.Fprintf(os.Stderr, "Hint: run 'bd formula list' to see available formulas\n")
+				os.Exit(1)
+			}
+		}
+
+		// Load the proto
+		protoIssue, err := store.GetIssue(ctx, protoID)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error loading proto %s: %v\n", protoID, err)
+			os.Exit(1)
+		}
+		if !isProtoIssue(protoIssue) {
+			fmt.Fprintf(os.Stderr, "Error: %s is not a proto (missing '%s' label)\n", protoID, MoleculeLabel)
+			os.Exit(1)
+		}
+
+		// Load the proto subgraph from DB
+		subgraph, err = loadTemplateSubgraph(ctx, store, protoID)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error loading proto: %v\n", err)
+			os.Exit(1)
 		}
 	}
 
-	protoID := protoIssue.ID
+	// Apply variable defaults from formula (gt-4v1eo)
+	vars = applyVariableDefaults(vars, subgraph)
 
-	// Verify it's a proto
-	if !isProtoIssue(protoIssue) {
-		cleanupCooked()
-		fmt.Fprintf(os.Stderr, "Error: %s is not a proto (missing '%s' label)\n", protoID, MoleculeLabel)
-		os.Exit(1)
-	}
-
-	// Load the proto subgraph
-	subgraph, err := loadTemplateSubgraph(ctx, store, protoID)
-	if err != nil {
-		cleanupCooked()
-		fmt.Fprintf(os.Stderr, "Error loading proto: %v\n", err)
-		os.Exit(1)
-	}
-
-	// Check for missing variables
-	requiredVars := extractAllVariables(subgraph)
+	// Check for missing required variables (those without defaults)
+	requiredVars := extractRequiredVariables(subgraph)
 	var missingVars []string
 	for _, v := range requiredVars {
 		if _, ok := vars[v]; !ok {
@@ -177,7 +208,6 @@ func runWispCreate(cmd *cobra.Command, args []string) {
 		}
 	}
 	if len(missingVars) > 0 {
-		cleanupCooked()
 		fmt.Fprintf(os.Stderr, "Error: missing required variables: %s\n", strings.Join(missingVars, ", "))
 		fmt.Fprintf(os.Stderr, "Provide them with: --var %s=<value>\n", missingVars[0])
 		os.Exit(1)
@@ -190,10 +220,6 @@ func runWispCreate(cmd *cobra.Command, args []string) {
 			newTitle := substituteVariables(issue.Title, vars)
 			fmt.Printf("  - %s (from %s)\n", newTitle, issue.ID)
 		}
-		if cookedProto {
-			fmt.Printf("\n  Note: Formula cooked inline as ephemeral proto.\n")
-		}
-		cleanupCooked()
 		return
 	}
 
@@ -201,32 +227,24 @@ func runWispCreate(cmd *cobra.Command, args []string) {
 	// bd-hobo: Use "wisp" prefix for distinct visual recognition
 	result, err := spawnMolecule(ctx, store, subgraph, vars, "", actor, true, "wisp")
 	if err != nil {
-		cleanupCooked()
 		fmt.Fprintf(os.Stderr, "Error creating wisp: %v\n", err)
 		os.Exit(1)
 	}
 
-	// Clean up ephemeral proto after successful spawn (bd-rciw)
-	cleanupCooked()
-
 	// Wisps are in main db but don't trigger JSONL export (Wisp flag excludes them)
 
 	if jsonOutput {
 		type wispCreateResult struct {
 			*InstantiateResult
-			Phase        string `json:"phase"`
-			CookedInline bool   `json:"cooked_inline,omitempty"`
+			Phase string `json:"phase"`
 		}
-		outputJSON(wispCreateResult{result, "vapor", cookedProto})
+		outputJSON(wispCreateResult{result, "vapor"})
 		return
 	}
 
 	fmt.Printf("%s Created wisp: %d issues\n", ui.RenderPass("✓"), result.Created)
 	fmt.Printf("  Root issue: %s\n", result.NewEpicID)
 	fmt.Printf("  Phase: vapor (ephemeral, not exported to JSONL)\n")
-	if cookedProto {
-		fmt.Printf("  Ephemeral proto cleaned up after use.\n")
-	}
 	fmt.Printf("\nNext steps:\n")
 	fmt.Printf("  bd close %s.<step>       # Complete steps\n", result.NewEpicID)
 	fmt.Printf("  bd mol squash %s         # Condense to digest (promotes to persistent)\n", result.NewEpicID)
@@ -243,6 +261,28 @@ func isProtoIssue(issue *types.Issue) bool {
 	return false
 }
 
+// resolvePartialIDDirect resolves a partial ID directly from store
+func resolvePartialIDDirect(ctx context.Context, partial string) (string, error) {
+	// Try direct lookup first
+	if issue, err := store.GetIssue(ctx, partial); err == nil {
+		return issue.ID, nil
+	}
+	// Search by prefix
+	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{
+		IDs: []string{partial + "*"},
+	})
+	if err != nil {
+		return "", err
+	}
+	if len(issues) == 1 {
+		return issues[0].ID, nil
+	}
+	if len(issues) > 1 {
+		return "", fmt.Errorf("ambiguous ID: %s matches %d issues", partial, len(issues))
+	}
+	return "", fmt.Errorf("not found: %s", partial)
+}
+
 var wispListCmd = &cobra.Command{
 	Use:   "list",
 	Short: "List all wisps in current context",